def main(self, checkpoint=None):
state = GenState(checkpoint=checkpoint,
sheep=self.s_toolbox.population(n=self.SHEEP_COUNT),
wolfs=self.w_toolbox.population(n=self.WOLFS_COUNT))
self.evaluate_population(state.sheep, state.wolfs)
state.log_population(0, self.v)
state.checkpoint(0)
for g in range(1, self.MAX_GEN):
state.sheep = self.s_toolbox.select(state.sheep, len(state.sheep))
state.wolfs = self.w_toolbox.select(state.wolfs, len(state.wolfs))
state.sheep = algorithms.varAnd(
state.sheep, self.common_tbx, self.S_CXPB,
0 if self.SHEEP_LAMARCK else self.S_MUTPB)
state.wolfs = algorithms.varAnd(
state.wolfs, self.common_tbx, self.W_CXPB,
0 if self.WOLFS_LAMARCK else self.W_MUTPB)
self.evaluate_population(state.sheep, state.wolfs)
state.log_population(g, self.v)
state.checkpoint(g)
if self.v:
print(state.s_hof)
print(state.w_hof)
return state
def gen_opt():
creator.create("FitnessMax", base.Fitness, weights=(1.0, ))
creator.create("Individual", list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register("population_guess", initPopulation, list,
creator.Individual)
# toolbox.register("evaluate", async_score)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutGaussian, mu=0, sigma=0.05, indpb=0.1)
toolbox.decorate("mate", checkBounds(0, 1))
toolbox.decorate("mutate", checkBounds(0, 1))
# toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population_guess()
update_id("experiment")
for gen in range(NGEN):
update_id("session")
print("New Generation: {}/{}".format(gen, NGEN))
offspring1 = algorithms.varAnd(random.sample(population, k=MU),
toolbox,
cxpb=CXPB,
mutpb=MUTPB)
offspring2 = algorithms.varAnd(population,
toolbox,
cxpb=CXPB,
mutpb=MUTPB)
population += offspring1 + offspring2
# 1st Turn
best = tournament(population, T1_POOL, T1_WIN)
# 2nd Turn
population = tournament(best, T2_POOL, T2_WIN, boss=True)
def main():
random.seed(64)
hosts = htoolbox.population(n=300)
parasites = ptoolbox.population(n=300)
hof = tools.HallOfFame(1)
hstats = tools.Statistics(lambda ind: ind.fitness.values)
hstats.register("avg", tools.mean)
hstats.register("std", tools.std)
hstats.register("min", min)
hstats.register("max", max)
column_names = ["gen", "evals"]
column_names.extend(hstats.functions.keys())
logger = tools.EvolutionLogger(column_names)
logger.logHeader()
MAXGEN = 50
H_CXPB, H_MUTPB = 0.5, 0.3
P_CXPB, P_MUTPB = 0.5, 0.3
fits = htoolbox.map(htoolbox.evaluate, hosts, parasites)
for host, parasite, fit in zip(hosts, parasites, fits):
host.fitness.values = parasite.fitness.values = fit
hof.update(hosts)
hstats.update(hosts)
logger.logGeneration(gen=0, evals=len(hosts), stats=hstats)
for g in range(1, MAXGEN):
hosts = htoolbox.select(hosts, len(hosts))
parasites = ptoolbox.select(parasites, len(parasites))
hosts = algorithms.varAnd(hosts, htoolbox, H_CXPB, H_MUTPB)
parasites = algorithms.varAnd(parasites, ptoolbox, P_CXPB, P_MUTPB)
fits = htoolbox.map(htoolbox.evaluate, hosts, parasites)
for host, parasite, fit in zip(hosts, parasites, fits):
host.fitness.values = parasite.fitness.values = fit
hof.update(hosts)
hstats.update(hosts)
logger.logGeneration(gen=g, evals=len(hosts), stats=hstats)
best_network = sn.SortingNetwork(INPUTS, hof[0])
print(best_network)
print(best_network.draw())
print("%i errors" % best_network.assess())
return hosts, hstats, hof
def main():
random.seed(64)
hosts = htoolbox.population(n=300)
parasites = ptoolbox.population(n=300)
hof = tools.HallOfFame(1)
hstats = tools.Statistics(lambda ind: ind.fitness.values)
hstats.register("avg", numpy.mean)
hstats.register("std", numpy.std)
hstats.register("min", numpy.min)
hstats.register("max", numpy.max)
logbook = tools.Logbook()
logbook.header = "gen", "evals", "std", "min", "avg", "max"
MAXGEN = 50
H_CXPB, H_MUTPB = 0.5, 0.3
P_CXPB, P_MUTPB = 0.5, 0.3
fits = htoolbox.map(htoolbox.evaluate, hosts, parasites)
for host, parasite, fit in zip(hosts, parasites, fits):
host.fitness.values = parasite.fitness.values = fit
hof.update(hosts)
record = hstats.compile(hosts)
logbook.record(gen=0, evals=len(hosts), **record)
print(logbook.stream)
for g in range(1, MAXGEN):
hosts = htoolbox.select(hosts, len(hosts))
parasites = ptoolbox.select(parasites, len(parasites))
hosts = algorithms.varAnd(hosts, htoolbox, H_CXPB, H_MUTPB)
parasites = algorithms.varAnd(parasites, ptoolbox, P_CXPB, P_MUTPB)
fits = htoolbox.map(htoolbox.evaluate, hosts, parasites)
for host, parasite, fit in zip(hosts, parasites, fits):
host.fitness.values = parasite.fitness.values = fit
hof.update(hosts)
record = hstats.compile(hosts)
logbook.record(gen=g, evals=len(hosts), **record)
print(logbook.stream)
best_network = sn.SortingNetwork(INPUTS, hof[0])
print(best_network)
print(best_network.draw())
print("%i errors" % best_network.assess())
return hosts, logbook, hof
def main():
random.seed(64)
hosts = htoolbox.population(n=300)
parasites = ptoolbox.population(n=300)
hof = tools.HallOfFame(1)
hstats = tools.Statistics(lambda ind: ind.fitness.values)
hstats.register("avg", numpy.mean)
hstats.register("std", numpy.std)
hstats.register("min", numpy.min)
hstats.register("max", numpy.max)
logbook = tools.Logbook()
logbook.header = "gen", "evals", "std", "min", "avg", "max"
MAXGEN = 50
H_CXPB, H_MUTPB = 0.5, 0.3
P_CXPB, P_MUTPB = 0.5, 0.3
fits = htoolbox.map(htoolbox.evaluate, hosts, parasites)
for host, parasite, fit in zip(hosts, parasites, fits):
host.fitness.values = parasite.fitness.values = fit
hof.update(hosts)
record = hstats.compile(hosts)
logbook.record(gen=0, evals=len(hosts), **record)
print(logbook.stream)
for g in range(1, MAXGEN):
hosts = htoolbox.select(hosts, len(hosts))
parasites = ptoolbox.select(parasites, len(parasites))
hosts = algorithms.varAnd(hosts, htoolbox, H_CXPB, H_MUTPB)
parasites = algorithms.varAnd(parasites, ptoolbox, P_CXPB, P_MUTPB)
fits = htoolbox.map(htoolbox.evaluate, hosts, parasites)
for host, parasite, fit in zip(hosts, parasites, fits):
host.fitness.values = parasite.fitness.values = fit
hof.update(hosts)
record = hstats.compile(hosts)
logbook.record(gen=g, evals=len(hosts), **record)
print(logbook.stream)
best_network = sn.SortingNetwork(INPUTS, hof[0])
print(best_network)
print(best_network.draw())
print("%i errors" % best_network.assess())
return hosts, logbook, hof
def run_algorithm(pop, cxpb, mutpb, ngen, stats):
for g in range(ngen):
state.generation = g
settings.output_statistics.write('\nGeneration {}\n\n'.format(g))
offspring = map(toolbox.clone, toolbox.select(pop, len(pop)))
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = []
for i, ind in enumerate(invalid_ind):
state.individual = i
fitness = toolbox.evaluate(ind)
fitnesses.append(fitness)
settings.output_statistics.write(
'Individiaul {} Fitness {} Price {} Edge {} Offset {}\n'.format(
i, fitness, ind[0], state.edges_list[int(ind[1]) % len(state.edges)], ind[2]))
settings.output_statistics.flush()
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
pop[:] = offspring
nevals = len(fitness)
record = stats.compile(pop)
logbook.record(gen=g, evals=nevals, **record)
settings.output_statistics.write('\n\n' + str(logbook) + '\n\n')
settings.output_statistics.flush()
def modifiedGA(population, toolbox, hallOfFame, n_neurons, trialAverage,
trialBest, cxpb, mutpb, ngen, game):
# Begin the generational process
for gen in range(1, ngen + 1):
# Select the next generation individuals
offspring = toolbox.select(population, len(population) - 1)
offspring.append(hallOfFame[0])
# Vary the pool of individuals
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
# Replace the current population by the offspring
population[:] = offspring
# MODIFIED BLOCK: Adds new agents based on the new offspring and goes through a game loop to set fitness values
game.reset()
for i in range(len(population)):
game.add_agent(Brain(population[i], n_neurons))
game.game_loop(display=False)
totalFitness = 0
largest = 0
for i in range(c.game['n_agents']):
totalFitness += g.agents[i].fitness
if g.agents[i].fitness > largest:
largest = g.agents[i].fitness
averageFitness = totalFitness / c.game['n_agents']
trialAverage.append(averageFitness)
trialBest.append(largest)
game.generation += 1
return population
def propagate(gens, ind, toolbox, pool, pop_size, cxpb, mutpb):
working_gen = gens[ind.gen]
asp_idx = [i for i, (a1, a2) in enumerate(working_gen.tournament_aspirants) if a1 == ind.pop_idx or a2 == ind.pop_idx]
for a in asp_idx:
a1, a2 = working_gen.tournament_aspirants[a]
if working_gen.pop[a1] and working_gen.pop[a2] and working_gen.pop[a1].fitness.valid and working_gen.pop[a2].fitness.valid:
working_gen.selected[a] = max(working_gen.pop[a1], working_gen.pop[a2], key=attrgetter('fitness'))
if a % 2 == 0:
start, stop = a, a + 2
else:
start, stop = a - 1, a + 1
if working_gen.selected[start] is not None and working_gen.selected[stop - 1] is not None and working_gen.offspring[start] is None and working_gen.offspring[stop - 1] is None:
working_gen.offspring[start:stop] = map(toolbox.clone, working_gen.selected[start:stop])
working_gen.offspring[start:stop] = algorithms.varAnd(working_gen.offspring[start:stop], toolbox, cxpb, mutpb)
if len(gens) <= ind.gen + 1:
gens.append(Generation(pop_size, tournament_aspirants=utils.generate_aspirant_pairs(pop_size), pop=[None] * pop_size))
gens[ind.gen + 1].pop[start:stop] = working_gen.offspring[start:stop] # comma selection
for idx, i in enumerate(gens[ind.gen + 1].pop[start:stop]):
i.pop_idx = start + idx
i.gen = ind.gen + 1
if not i.fitness.valid and i.pop_idx in gens[i.gen].aspirants:
pool.submit(i, order=(i.gen, gens[i.gen].aspirant_order[i.pop_idx]))
gens[i.gen].waiting.add(i.pop_idx)
else:
propagate(gens, i, toolbox, pool, pop_size, cxpb, mutpb)
def GA(toolbox, cxpb=0.5, mutpb=0.2, ngen=40, mu=2000, *args, **kwargs):
'''
'''
stats, logbook, record, pop, hof = initMisc(toolbox, npop=mu, nhof=100, similar=np.array_equal)
# Begin the generational process
for gen in range(1, ngen + 1):
# Select the next generation individuals
offspring = toolbox.select(pop, len(pop))
# Vary the pool of individuals
offspring = varAnd(offspring, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Update the hall of fame with the generated individuals
hof.update(offspring)
if kwargs.has_key('callback'):
kwargs['callback'](1, p=hof[0])
# Replace the current population by the offspring
pop[:] = offspring
# Append the current generation statistics to the logbook
record = stats.compile(pop) if stats else {}
logbook.record(gen=gen, nevals=len(invalid_ind), **record)
print logbook.stream
print "Best individual is ", hof[0].fitness.values[0]
if len(hof[0]) < 20:
print hof[0]
return {'x':hof[0],
'population':pop,
'stats':stats,
'hof':hof,
}
def eaSimplePlusElitism(population,
toolbox,
cxpb,
mutpb,
eprop,
ngen,
stats=None,
halloffame=None,
verbose=__debug__):
"""
Variante de `deap.algorithms.eaSimple` con una proporción de elitismo.
"""
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
# Evalua los individuos con aptitud inválida.
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
logbook.record(gen=0, nevals=len(invalid_ind), **record)
if verbose:
print(logbook.stream)
# Comienza el proceso evolutivo.
for gen in range(1, ngen + 1):
# Seleccina la próxima generación de individuos.
offspring = toolbox.select(population, len(population))
# Varia el pool de individuos, aplicando cruza y mutación.
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
# Evalua los individuos con aptitud inválida.
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Actualiza el grupo de mejores individuos.
if halloffame is not None:
halloffame.update(offspring)
# Reemplaza la población actual con los mejores del conjunto
# compuesta por su descendencia y la elite.
elite_count = int(len(population) * eprop)
elite = tools.selBest(population, elite_count)
population[:] = tools.selBest(offspring + elite, len(population))
# Toma nota de las estadísticas de la generación actual.
record = stats.compile(population) if stats else {}
logbook.record(gen=gen, nevals=len(invalid_ind), **record)
if verbose:
print(logbook.stream)
return population, logbook
def DoSingleIterGA_SHGMaximize (self, remeasure=True) : """ Perform a single iteration of GA to find phase of laser pulse that coherently suppresses single sample fluorescence """ wx.Yield() # abort, if requested if self.need_abort : return if remeasure : # Record spectrum self.optimization_pop = self.MeasureSpectra(self.optimization_pop) wx.Yield() # abort, if requested if self.need_abort : return # Calculate the fitness the population for ind in self.optimization_pop : ind.fitness.values = (ind.spectra.sum(),) self.optimization_pop[:] = self.optimization_toolbox.select( self.optimization_pop, self.population_size ) else : # Generate offspring offspring = algorithms.varAnd(self.optimization_pop, self.optimization_toolbox, self.cxpb, self.mutpb) # Measure spectra for offspring only offspring = self.MeasureSpectra(offspring) wx.Yield() # abort, if requested if self.need_abort : return # Calculate the fitness of offspring for ind in offspring : ind.fitness.values = (ind.spectra.sum(),) self.optimization_pop[:] = self.optimization_toolbox.select( self.optimization_pop + offspring, int(1.2*self.population_size) ) wx.Yield() # abort, if requested if self.need_abort : return # Saving statistics for plotting purposes for key, value in self.optimization_stats.compile(self.optimization_pop).items() : try : self.optimization_log[key].append(value) except KeyError : self.optimization_log[key] = [value] self.SaveOptimization() self.DisplayOptimization() # Going to the next iteration wx.CallAfter (self.DoSingleIterGA_SHGMaximize, remeasure=(not remeasure))
def generate_word(word, letters, population_size):
creator.create("Fitness", base.Fitness, weights=(-1.0,))
creator.create("Individual", list, fitness=creator.Fitness)
toolbox = base.Toolbox()
toolbox.register("attr_bool", generate_letter, letters=letters)
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_bool, n=len(word))
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", evaluate_alphabet_distance, word=word, alphabet=letters)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", mutInAlphabet, letters=letters, max_step=3, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=population_size)
generation = 0
while have_not_found_yet(population, generation, word):
offspring = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
generation += 1
if generation % 100 == 0:
print(generation)
print(generation)
print(tools.selBest(population, k=1)[0])
def _do_generation(self, pop, gen_num, logbook):
"""Implement a generation of the search process.
:param pop: The population
:type pop: Any iterable type
:param gen_num: The generation number
:type gen_num: :py:class:`int`
:param logbook: Logbook for the stats
:type logbook: :py:class:`~deap.tools.Logbook`
"""
# Select the next generation individuals
offspring = self._toolbox.select(pop, self.pop_size)
# Vary the pool of individuals
offspring = varAnd(offspring, self._toolbox, self.xover_pb,
self.mut_pb)
# Evaluate the individuals with an invalid fitness
num_evals = self._eval(offspring)
# Replace the current population by the offspring
pop[:] = offspring
# Append the current generation statistics to the logbook
self._do_stats(pop, gen_num, num_evals, logbook)
def _execute(self) -> list:
"""
Запуск алгоритма.
Потомок offspring - с вероятностью cxpb 2 подряд идущих в списке индивида скрещиваются
и их дети заменяют родителей, а с вероятностью mutpb после процесса скрещивания каждый индивид мутирует.
Далее рассчитывается ценность каждого потомка и рассчитанные ценности
заполняют поля ценности (values) в соответствующих индивидах.
Затем отбор нового поколения.
В конце - выбор лучшего
:return:
"""
population = self._toolbox.population(n=self.START_POPULATION_SIZE)
for gen in range(self.GENERATION_COUNT):
offspring = algorithms.varAnd(population,
self._toolbox,
cxpb=self.CROSSOVER_CHANCE,
mutpb=self.MUTATE_CHANCE)
fits = self._toolbox.map(self._toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = self._toolbox.select(offspring, k=len(population))
top1 = tools.selBest(population, k=1)
return top1[0]
def _run_evolution(self):
creator.create("FitnessMax", base.Fitness, weights=(1.0, ))
creator.create("Individual", list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register("attr_bool", random.randint, 0, 1)
toolbox.register("individual",
tools.initRepeat,
creator.Individual,
toolbox.attr_bool,
n=100)
toolbox.register("population", tools.initRepeat, list,
toolbox.individual)
toolbox.register("evaluate", self._eval_evolution_by_loss)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=300)
NGEN = 40
for gen in range(NGEN):
offspring = algorithms.varAnd(population,
toolbox,
cxpb=0.5,
mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
top10 = tools.selBest(population, k=10)
return top10
def approximate(func, base_range, bounds, population_size, generations):
def evaluation_func(individual):
score = 0.0
for idx, x in enumerate(base_range):
score += abs(func(x) - individual[idx])
return score,
creator.create("Fitness", base.Fitness, weights=(-1.0,))
creator.create("Individual", list, fitness=creator.Fitness)
toolbox = base.Toolbox()
toolbox.register("attr_bool", float_between, *bounds)
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_bool, n=len(base_range))
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", evaluation_func)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=population_size)
for gen in range(generations):
offspring = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
show_best_individual(base_range, func, population)
def run_evolution(generations=10):
toolbox.register("evaluate", eval_diff_fitness)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=20)
fit_history = []
for gen in range(generations):
print(f'gen # {gen}')
offspring = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
fit_values = []
for ind in population:
fitness = ind.fitness.values
fit_values.append(fitness)
fit_history.append(np.average(fit_values))
top10 = tools.selBest(population, k=10)
return top10, fit_history
def learn(self):
""" Runs genetic algorithms.
By using DEAP, generates an initial population and runs for n generations.
Returns:
A dict with the features weight and others params.
"""
solution = {}
# Generate Population
population = self.deap_toolbox.population(n=self.population)
# Evolve
for gen in range(self.generations):
offspring = algorithms.varAnd(population, self.deap_toolbox, cxpb=0.5, mutpb=0.1)
fits = self.deap_toolbox.map(self.deap_toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = self.deap_toolbox.select(offspring, k=len(population))
# Select best
best = tools.selBest(population, k=1)[0]
best_fitness, = self.fitness_wrapper(best)
revisions_weight, fixes_weight, authors_weight = self.decode_individual(best)
solution["revisions"] = revisions_weight
solution["fixes"] = fixes_weight
solution["authors"] = authors_weight
solution["fitness"] = best_fitness
solution["bits"] = self.bits
solution["generations"] = self.generations
return solution
def run(self):
breakEarly = False
for gen in range(1, self.NGEN + 1):
try:
if breakEarly:
print("Stopped by user!")
break
offsprings = algorithms.varAnd(self.population,
self.toolbox,
cxpb=MathFunGA.CXPB,
mutpb=MathFunGA.MUTPB)
fitnesses = self.toolbox.map(self.toolbox.evaluate, offsprings)
for fit, ind in zip(fitnesses, offsprings):
ind.fitness.values = fit
self.population = self.toolbox.select(offsprings,
k=len(self.population))
theBestThisPop = tools.selBest(self.population, k=1)[0]
theBestFitness = theBestThisPop.fitness.getValues()[0]
print((str(gen) + ":").ljust(5) + str(theBestFitness))
if theBestFitness < MathFunGA.FITNESS_TARGET:
print("Satisfying fitness reached!")
break
except KeyboardInterrupt:
breakEarly = True
else:
print("Maximum number of iterations reached!")
self.showResults()
def seqSelectionRound(sess, population, toolbox, args): offspring = algorithms.varAnd(population, toolbox, cxpb=args['cspb'], mutpb=args['mutpb']) fits = evaluateThese(sess, offspring,args); for fit, ind in zip(fits, offspring): ind.fitness.values = fit population = toolbox.select(offspring, k=len(population)) return (population);
def run_algorithm(pop, cxpb, mutpb, ngen, stats):
for g in range(ngen):
state.generation = g
settings.output_statistics.write('\nGeneration {}\n\n'.format(g))
offspring = map(toolbox.clone, toolbox.select(pop, len(pop)))
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = []
for i, ind in enumerate(invalid_ind):
state.individual = i
fitness = toolbox.evaluate(ind)
fitnesses.append(fitness)
settings.output_statistics.write(
'Individiaul {} Fitness {} Price {} Edge {} Offset {}\n'.
format(i, fitness, ind[0],
state.edges_list[int(ind[1]) % len(state.edges)],
ind[2]))
settings.output_statistics.flush()
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
pop[:] = offspring
nevals = len(fitness)
record = stats.compile(pop)
logbook.record(gen=g, evals=nevals, **record)
settings.output_statistics.write('\n\n' + str(logbook) + '\n\n')
settings.output_statistics.flush()
def update(self, *args):
self.canvas.clear()
self.epoch += 1
top10 = tools.selBest(self.population, k=1)
elite = top10[0]
offspring = algorithms.varAnd(self.population,
toolbox,
cxpb=1.0,
mutpb=0.7)
fits = list(toolbox.map(toolbox.evaluator, offspring))
for fit, ind in zip(fits, offspring):
ind.fitness.values = [fit]
self.population = toolbox.select(offspring, k=self.pops)
self.population[0] = elite
top10 = tools.selBest(self.population, k=1)
top_v, top = eval_f(top10[0], True)
with self.canvas:
Color(rgba=(1, 0.8, 0.1, 0.7))
for x, y in zip(top[0], top[1]):
Ellipse(pos=(x, y), size=(5, 5))
self.label = Label(text="{:.2f} : {}".format(
float(top_v), self.epoch),
halign="right")
def eaSimpleConverge(population, toolbox, cxpb, mutpb, ngen, stats=None,
halloffame=None, verbose=True):
"""This algorithm reproduce the simplest evolutionary algorithm as
presented in chapter 7 of [Back2000]_.
Modified to allow checking if there is no change for ngen, as a simple
rule for convergence. Interface is similar to eaSimple(). However, in
eaSimple, ngen is total number of iterations; in eaSimpleConverge, we
terminate only when the best is NOT updated for ngen iterations.
"""
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
# Begin the generational process
gen = 1
best = 0
while True:
# Select the next generation individuals
offspring = toolbox.select(population, len(population))
# Vary the pool of individuals
offspring = varAnd(offspring, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
# Replace the current population by the offspring
population[:] = offspring
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
current_best = record['max']
if gen % 20 == 0 and verbose:
print >> sys.stderr, "Current iteration {0}: max_score={1}".\
format(gen, current_best)
if current_best != best:
best = current_best
updated = gen
gen += 1
if gen - updated > ngen:
break
return population
def test_pheromone_mode(self):
toolbox = self.toolbox
toolbox.register("select",
tigerMosquitoSelection,
tournsize=3,
useFitness=False)
population = toolbox.population(n=3)
# population size = 3
offspring = algorithms.varAnd(population, toolbox, cxpb=0., mutpb=0.)
# set pheromone each individual
pheromones = [50, 100, 75]
# evaluation
fits = toolbox.map(toolbox.evaluate, offspring)
max_p = -1
for i, fit_ind in enumerate(zip(fits, offspring)):
fit, ind = fit_ind
ind.fitness.values = fit
ind.pheromone.values = (pheromones[i], )
if max_p <= pheromones[i]:
max_p = pheromones[i]
max_sample = ind
random.seed(20180719)
selected_ind = toolbox.select(offspring, k=1)
self.assertEqual([[1, 1, 0]], selected_ind)
def compose(toolbox, window, tonic):
global chords_in_vector
population = toolbox.population(n=pop_size)
NGEN = num_gens
for gen in range(NGEN):
offspring = algorithms.varAnd(population, toolbox, cxpb=cx_pb, mutpb=mut_pb)
fits = toolbox.map(toolbox.evaluate, offspring)
total_fitness = 0
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
total_fitness += fit
population = toolbox.select(offspring, k=len(population))
#print("Total fitness in gen %s : %s" % (gen, total_fitness))
#print("Best : %s" % evaluate(tools.selBest(population, k=1)[0]))
top = tools.selBest(population, k=1)[0]
np.set_printoptions(threshold=np.nan)
#pprint("%s, %s" % (window, top))
#pprint(evaluate(top))
return top, evaluate(top)
def eaSimpleWithElitism(population,
toolbox,
cxpb,
mutpb,
ngen,
stats=None,
halloffame=None,
verbose=__debug__):
#подготовка исходных данных для генерации
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
# сравнение единиц с не валидным фитнес значением
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if halloffame is None:
raise ValueError("halloffame parameter must not be empty!")
halloffame.update(population)
hof_size = len(halloffame.items) if halloffame.items else 0
record = stats.compile(population) if stats else {}
logbook.record(gen=0, nevals=len(invalid_ind), **record)
if verbose:
print(logbook.stream)
# Начало процесса генерации
for gen in range(1, ngen + 1):
# выборка следующего поколения единиц
offspring = toolbox.select(population, len(population) - hof_size)
#отклонение поколения
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
# сравнение единиц с не валидным фитнес значением
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# возвращение лучшего значения популяции
offspring.extend(halloffame.items)
# дополненией результата новым поколением
halloffame.update(offspring)
#замещение старой популяции новой
population[:] = offspring
# обновление и вывод статистики
record = stats.compile(population) if stats else {}
logbook.record(gen=gen, nevals=len(invalid_ind), **record)
if verbose:
print(logbook.stream)
return population, logbook
def nsga(population, start_gen, toolbox, cxpb, mutpb, ngen,
stats, halloffame, logbook, verbose, exp_id=None):
eval_invalid_inds = (
eval_invalid_inds_single_gpu
if Config.GPU
else eval_invalid_inds_cpu_parallel
)
popsize = len(population)
total_time = datetime.timedelta(seconds=0)
eval_invalid_inds(population, toolbox)
for gen in range(start_gen, ngen):
start_time = datetime.datetime.now()
offspring = algorithms.varAnd(population, toolbox, cxpb=cxpb,
mutpb=mutpb)
evals = eval_invalid_inds(offspring, toolbox)
population = toolbox.select(population+offspring, k=popsize)
halloffame.update(offspring) # updates pareto front
# update statics
record = stats.compile(population)
logbook.record(gen=gen, evals=evals, **record)
if verbose:
print(logbook.stream, flush=True)
# save checkpoint
if gen % 1 == 0:
# Fill the dictionary using the dict(key=value[, ...]) constructor
cp = dict(
population=population,
generation=gen,
halloffame=halloffame,
logbook=logbook,
rndstate=random.getstate(),
config=Config,
)
if exp_id is None:
cp_name = "checkpoint_nsga.pkl"
else:
cp_name = "checkpoint_nsga_{}.pkl".format(exp_id)
pickle.dump(cp, open(cp_name, "wb"))
# check hard time limit
gen_time = datetime.datetime.now() - start_time
total_time = total_time + gen_time
print("Time ", total_time)
# hard time limit was necessary at metacentrum
#
# if total_time > datetime.timedelta(hours=4*24):
# print("Time limit exceeded.")
# break
return population, logbook
def runExample():
args = {'sequence_length' : 110 , 'nucleotide_frequency' : [0.25,0.25,0.25,0.25], 'mutation_frequency' : 0.05 }
np.random.seed(1239571243);
randomizer=np.random
creator.create("FitnessMax", base.Fitness, weights=(1.0,))
creator.create("Individual", list , fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register("base", getRandomBase, randomizer, args)
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.base, n=args['sequence_length'])
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", fitness, "ATGC")
#toolbox.register("evaluate", fitness)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", mutateSequence, randomizer, args)
#toolbox.register("mutate", mutateSequence, args['mutation_frequency'])
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=300)
NGEN=1000
for gen in range(NGEN):
offspring = algorithms.varAnd(population, toolbox, cxpb=0.1, mutpb=0.1)
#offspring = algorithms.varAnd(population, toolbox, cxpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
print(type(fits))
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
top10 = tools.selBest(population, k=10)
return(top10);
def findNominalValues(self):
nominalVals = []
for evalMode in self.model.modes:
nominalValsMode = []
self.toolbox.register("evaluate", evalMode)
#initialize new random population
self.popu = self.toolbox.population(self.populationSize)
for gen in range(self.NGEN):
print(gen)
#generate offspprings with crossover and mutations
offspring = algorithms.varAnd(self.popu,
self.toolbox,
cxpb=0.5,
mutpb=0.75)
#evaluate individuals
fits = self.toolbox.map(self.toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
if self.model.isViable(ind) and ind not in nominalValsMode:
nominalValsMode.append(ind)
ind.fitness.values = fit
#roulete wheel selection
self.popu = self.toolbox.select(offspring, k=len(self.popu))
print("Number of viable points: " + str(len(nominalValsMode)))
nominalVals.extend(nominalValsMode)
return nominalVals
def geneticAlgorithmWithEvalFunctional(base_func, eval_func, search_region, population_size, generations, **args):
creator.create("Fitness", base.Fitness, weights=(-1.0,))
creator.create("Individual", list, fitness=creator.Fitness)
toolbox = base.Toolbox()
toolbox.register("attr_bool", float_between, *search_region)
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_bool, n=1)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", eval_func, **args)
toolbox.register("mate", skippingCrosover)
(a, b) = search_region
toolbox.register("mutate", mutInRegion, a=a, b=b, max_step=0.1, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=population_size)
for gen in range(generations):
offspring = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
print(tools.selBest(population, k=1))
base_range = float_range(*search_region)
plot(base_range, [base_func(x) for x in base_range], 'r')
show()
def GetBetters(self):
self.toolbox.register("evaluate", self.EvalOneMax)
self.toolbox.register("mate", tools.cxTwoPoint) # crossover
self.toolbox.register("mutate", tools.mutFlipBit,
indpb=0.05) # mutação
self.toolbox.register("select", tools.selTournament, tournsize=3)
population = self.toolbox.population(n=300)
NGEN = 40
for gen in range(NGEN):
offspring = algorithms.varAnd(population,
self.toolbox,
cxpb=0.5,
mutpb=0.1)
fits = self.toolbox.map(self.toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
if fit['weight'] > self.limit:
ind.fitness.values = [0]
else:
ind.fitness.values = fit['value']
population = self.toolbox.select(offspring, k=len(population))
betters = tools.selBest(population, k=10)[0]
result = []
for key, value in enumerate(betters):
if value == 1:
result.append(self.products[key])
return {"products": result, "state": self.EvalOneMax(betters)}
def startalgrithm(topk):
liststring = input("pls input the list, saperate with , :")
for item in liststring.split(','):
listinput.append(int(item))
creator.create("FitnessMax", base.Fitness, weights=(1,)) #weights
creator.create("Individual", list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register("attr_bool", random.randint, -1, 1) # value range
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_bool, n=len(listinput)) #number of parameters
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", evalOneMax)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=300)
NGEN=40
for gen in range(NGEN):
offspring = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
topk = input("pls input the number of result:")
top2 = tools.selBest(population, k=int(topk)) #top1
return top2
def example_nevzpominam():
# Creating appropriate type
creator.create("FitnessMax", base.Fitness, weights=(1.0,))
creator.create("Individual", list, fitness=creator.FitnessMax)
# Initialization
IND_SIZE = 100
toolbox = base.Toolbox()
toolbox.register("attr_bool", random.randint, 0, 1)
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_bool, n=IND_SIZE)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", evalOneMax)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=300)
NGEN=40
for gen in range(NGEN):
offspring = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
top10 = tools.selBest(population, k=10)
def genetic(self, n_epochs=40):
creator.create("FitnessMax", base.Fitness, weights=(-1.0, ))
creator.create("Individual", np.ndarray, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register("attr_float", np.random.random)
toolbox.register("individual",
tools.initRepeat,
creator.Individual,
toolbox.attr_float,
n=self.M)
toolbox.register("population", tools.initRepeat, list,
toolbox.individual)
def eval_def(individual):
return self.rmse_loss(self.X_train @ individual),
toolbox.register("evaluate", eval_def)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
population = toolbox.population(n=300)
for gen in range(n_epochs):
offspring = algorithms.varAnd(population,
toolbox,
cxpb=0.5,
mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
self.w = tools.selBest(population, k=1)[0]
def main(procid, pipein, pipeout, sync, run_num, config,vseed=None):
#random.seed(seed)
toolbox.register("migrate", migPipe, k=5, pipein=pipein, pipeout=pipeout,
selection=tools.selBest, replacement=random.sample)
MU = config["POPULATION_SIZE"]
NGEN = 500
CXPB = 0.5
MUTPB = 0.2
MIG_RATE = 5
deme = toolbox.population(n=MU)
hof = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", numpy.mean)
stats.register("std", numpy.std)
stats.register("min", numpy.min)
stats.register("max", numpy.max)
logbook = tools.Logbook()
logbook.header = "gen", "deme", "evals", "std", "min", "avg", "max"
for ind in deme:
ind.fitness.values = toolbox.evaluate(ind)
record = stats.compile(deme)
logbook.record(gen=0, deme=procid, evals=len(deme), **record)
hof.update(deme)
# if procid == 0:
# # Synchronization needed to log header on top and only once
# print run_num, logbook.stream
# sync.set()
# else:
# logbook.log_header = False # Never output the header
# print run_num, logbook.stream
# sync.wait()
for gen in range(1, NGEN):
deme = toolbox.select(deme, len(deme))
deme = algorithms.varAnd(deme, toolbox, cxpb=CXPB, mutpb=MUTPB)
invalid_ind = [ind for ind in deme if not ind.fitness.valid]
for ind in invalid_ind:
ind.fitness.values = toolbox.evaluate(ind)
hof.update(deme)
record = stats.compile(deme)
logbook.record(gen=gen, deme=procid, evals=len(deme), **record)
r = "%d,%d,%d,%d,%d" % (run_num,procid, gen, len(deme), record['max'])
print r
if record['max']>=128:
#print run_num, "FOUND"
return
if gen % MIG_RATE == 0 and gen > 0:
toolbox.migrate(deme)
def evolve_stage1(self, cxpb, mutpb, n_gen=50, k_elites=1, w_ssv=None):
"""
Perform stage 1 evolution, where only the local fitness (number of false states) matters.
In this stage, each gene's regulation function is evolved separately and not cooperation is needed.
:param cxpb: cross-over probability
:param mutpb: mutation probability
:param n_gen: number of generations
:param k_elites: number of elites
:param w_ssv: penalty weight of stable state violations. If None, then no penalty.
:return:
"""
self.stage = 1
self.n_gen_stage1 = n_gen
if n_gen == 0:
return
# normal single-objective GP
self.toolbox.register('select', tools.selTournament, tournsize=3)
self.toolbox.register('evaluate', self._evaluate_stage1, w_ssv=w_ssv)
FitnessMin.weights = (-1.0, )
for gen in range(n_gen + 1):
self.gen = gen
# individuals that have been changed due to mutation or crossover
invalid_pop = [
ind for ind in self.population if not ind.fitness.valid
]
self._compile(invalid_pop)
if self.stable_states is not None:
self._count_stable_state_violations(invalid_pop)
self._count_num_regulators(invalid_pop)
# Evaluate the individuals with an invalid fitness
fitnesses = self.toolbox.map(self.toolbox.evaluate, invalid_pop)
for ind, fit in zip(invalid_pop, fitnesses):
ind.fitness.values = fit
self.hof_stage1.update(self.population)
self.best_local_fitness = max(
self.population, key=lambda ind: ind.fitness).fitness.values[0]
# log
if hasattr(self, 'logbook'):
record = self.mstats.compile(self.population)
self.logbook.record(index=self.index,
stage=self.stage,
gen=self.gen,
**record)
self._log_to_file()
if gen == n_gen:
break
# selection and variation to produce the next generation
elites = tools.selBest(self.population, k_elites)
parents = self.toolbox.select(self.population,
len(self.population) - k_elites)
offspring = algorithms.varAnd(parents,
toolbox=self.toolbox,
cxpb=cxpb,
mutpb=mutpb)
self.population = elites + offspring
def main():
if os.path.isfile(CP):
# A file name has been given, then load the data from the file
cp = read_checkpoint()
population = cp["population"]
start_gen = cp["generation"] + 1
halloffame = cp["halloffame"]
logbook = cp["logbook"]
random.setstate(cp["rndstate"])
else:
# Start a new evolution
random.seed()
population = toolbox.population(n=300)
start_gen = 0
halloffame = tools.HallOfFame(maxsize=1)
logbook = tools.Logbook()
stats_fit = tools.Statistics(lambda ind: ind.fitness.values)
stats_size = tools.Statistics(len)
mstats = tools.MultiStatistics(fitness=stats_fit, size=stats_size)
mstats.register("avg", numpy.mean)
mstats.register("std", numpy.std)
mstats.register("min", numpy.min)
mstats.register("max", numpy.max)
#algorithms.eaSimple(pop, toolbox, 0.5, 0.2, NGEN, mstats, halloffame=hof)
#print(hof[0])
begin = start_gen
end = begin + NGEN
print("begin: {}, end: {}".format(begin, end))
for gen in range(begin, end):
population = algorithms.varAnd(population,
toolbox,
cxpb=toolbox.mate,
mutpb=toolbox.mutate)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
halloffame.update(population)
record = mstats.compile(population)
logbook.record(gen=gen, evals=len(invalid_ind), **record)
population = toolbox.select(population, k=len(population))
if (gen + 1) % FREQ == 0 or gen == end - 1:
# Fill the dictionary using the dict(key=value[, ...]) constructor
cp = dict(population=population,
generation=gen,
halloffame=halloffame,
logbook=logbook,
rndstate=random.getstate())
with open(CP, "wb") as cp_file:
pickle.dump(cp, cp_file, -1)
def compose(params):
global window, chords_in_vector
start = time()
pop_size = 35 # int(params[0])
num_gens = 65 # int(params[1])
tourn_size = int(params[0])
ind_pb = params[1]
cx_pb = params[2]
mut_pb = params[3]
creator.create("FitnessMulti", base.Fitness, weights=(-1.0, 1.0))
creator.create("Individual", list, fitness=creator.FitnessMulti)
toolbox = base.Toolbox()
IND_SIZE = chords_in_vector - len(window)
toolbox.register("attr_chord", cg.generate_chord)
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_chord, n=IND_SIZE)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
toolbox.register("evaluate", predict)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", mutate_individual, indpb=ind_pb)
toolbox.register("select", tools.selTournament, tournsize=tourn_size)
population = toolbox.population(n=pop_size)
NGEN = num_gens
for gen in range(NGEN):
offspring = algorithms.varAnd(population, toolbox, cxpb=cx_pb, mutpb=mut_pb)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
top = tools.selBest(population, k=1)[0]
np.set_printoptions(threshold=np.nan, suppress=True)
#pprint("%s, %s" % (window, top))
#pprint(predict(top))
score = predict(top)
end = time()
run_time = end - start
#time_dist = power(absolute(20 - run_time), 2) + 1
#f = -log(score[1] / time_dist)
f = -log(score[1]) * 100000000
print(params)
print("{:2.10f}".format(f))
results.append([list(params), f])
return f
def eaSimpleCustom(population,
toolbox,
cxpb,
mutpb,
sgen=1,
ngen=1,
stats=None,
halloffame=None,
verbose=__debug__):
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = eval_exec_async(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(population)
log_hof(sgen, halloffame)
record = stats.compile(population) if stats else {}
logbook.record(gen=sgen, nevals=len(invalid_ind), **record)
if verbose:
log_stats(logbook.stream)
# Begin the generational process
for gen in range(sgen, ngen + 1):
# Select the next generation individuals
offspring = toolbox.select(population, len(population))
# Vary the pool of individuals
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = eval_exec_async(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
log_hof(gen, halloffame)
# Replace the current population by the offspring
population[:] = offspring
population_persist(population, gen)
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
logbook.record(gen=gen, nevals=len(invalid_ind), **record)
if verbose:
log_stats(logbook.stream)
return population, logbook
def evolve(population,
toolbox,
cxpb,
mutpb,
ngen,
stats=None,
halloffame=None,
verbose=__debug__):
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
logbook.record(gen=0, nevals=len(invalid_ind), **record)
if verbose:
print logbook.stream
# Begin the generational process
for gen in range(1, ngen + 1):
# Select the next generation individuals
offspring = toolbox.select(population, len(population))
# Vary the pool of individuals
offspring = varAnd(offspring, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
# Replace the current population by the offspring
population[:] = offspring
# elitism
t = random.randint(0, len(population) - 1)
# t = 0
population[t] = halloffame[0]
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
logbook.record(gen=gen, nevals=len(invalid_ind), **record)
if verbose:
print logbook.stream
return population, logbook
def run_ea(fitness_function, time_function, max_evals, max_gen, n_cpus=50, pop_size=100, cxpb = 0.8, mutpb= 0.1):
toolbox = create_toolbox(fitness_function)
initial_pop = toolbox.population(n=pop_size)
aspirant_pairs = utils.generate_aspirant_pairs(pop_size)
pool = ParallelSimulator(n_cpus=n_cpus, eval_func=toolbox.evaluate, time_func=time_function)
start = datetime.datetime.now()
last = start
gens = [Generation(pop_size, tournament_aspirants=aspirant_pairs, pop=initial_pop)]
t = 0
best_ind = None
while pool.evals < max_evals:
# submit individuals for current generation
for idx, ind in enumerate(gens[t].pop):
if not ind.fitness.valid:
ind.pop_idx = idx
pool.submit(ind)
while not pool.all_evaluations_finished():
result = pool.next_finished()
ind = result.args[0]
gens[t].pop[ind.pop_idx].fitness.values = result.value
if not best_ind or ind.fitness > best_ind.fitness:
best_ind = ind
pop = gens[t].pop
# finish tournament selection
gens[t].selected = [max(pop[asp1], pop[asp2], key=attrgetter('fitness')) for asp1, asp2 in gens[t].tournament_aspirants]
# run operators
gens[t].offspring = map(toolbox.clone, gens[t].selected)
gens[t].offspring = algorithms.varAnd(gens[t].offspring, toolbox, cxpb, mutpb)
# create next generation
gens.append(Generation(pop_size, tournament_aspirants=utils.generate_aspirant_pairs(pop_size), pop=gens[t].offspring[:]))
t += 1
# print logging information every second
now = datetime.datetime.now()
if now - last > datetime.timedelta(seconds=1):
runtime = (now - start).total_seconds()
print('TIME:', runtime, 'SPEED:', pool.evals / runtime)
last = now
end = datetime.datetime.now()
print(pool.evals / (end - start).total_seconds())
print(pool.evals)
print(pool.current_time)
pool.print_stats()
return best_ind, pool.log
def eaSimpleModified(population, toolbox, cxpb, mutpb, ngen, stats=None,
halloffame=None, verbose=__debug__):
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
logbook.record(gen=0, nevals=len(invalid_ind), **record)
if verbose:
print(logbook.stream)
best = []
best_ind = max(population, key=attrgetter("fitness"))
best.append(best_ind)
# Begin the generational process
for gen in range(1, ngen + 1):
# Select the next generation individuals
offspring = toolbox.select(population, len(population))
# Vary the pool of individuals
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Save the best individual from the generation
best_ind = max(offspring, key=attrgetter("fitness"))
best.append(best_ind)
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
# Replace the current population by the offspring
population[:] = offspring
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
logbook.record(gen=gen, nevals=len(invalid_ind), **record)
if verbose:
print(logbook.stream)
return population, logbook, best
def eaSimpleWarp(population, toolbox, filename, cxpb, mutpb, ngen, stats=None,
halloffame=None, verbose=__debug__, labels=None):
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
# Evaluate the individuals with an invalid fitness
# TODO: Change fitness evaluation to operate on the population not on individuals
# TODO because all fitnesses are returned from WARP we need to pass all to the batch script simulatneously
# TODO and then wait.
# generate_fitnesses(population, toolbox)
# Find which individuals have no fitness assigned (probably all of them here)
fitnesses = return_efficiency(population, 'generation_0')
print fitnesses
# Assign new fitness values to the individuals
for ind, fit in zip(population, fitnesses):
ind.fitness.values = (fit,)
# Update HoF
if halloffame is not None:
halloffame.update(population)
save_generation(filename, population, generation=0, labels=None)
# Begin the generational process
for gen in range(1, ngen + 1):
print "Starting Generation: {}".format(gen)
# Select the next generation individuals
offspring = toolbox.select(population, len(population))
# Vary the pool of individuals
offspring = varAnd(offspring, toolbox, cxpb, mutpb)
# ######################## Start server setup routine ##################################################
# ######################## End server setup routine ####################################################
fitnesses = return_efficiency(offspring, 'generation_{}'.format(gen))
for ind, fit in zip(offspring, fitnesses):
ind.fitness.values = (fit,)
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
# Replace the current population by the offspring
population[:] = offspring
# Append the current generation statistics to the logbook and save data file
save_generation(filename, population, generation=gen, labels=None)
# record = stats.compile(population) if stats else {}
# logbook.record(gen=gen, nevals=len(invalid_ind), **record)
# if verbose:
# print logbook.stream
print "Completed Generation: {}".format(gen)
# TODO switch return back to population
return offspring, logbook
def main(extended=True, verbose=True):
target_set = []
species = []
stats = tools.Statistics(lambda ind: ind.fitness.values, n=TARGET_TYPE)
stats.register("avg", tools.mean)
stats.register("std", tools.std)
stats.register("min", min)
stats.register("max", max)
if verbose:
column_names = ["gen", "species", "evals"]
column_names.extend(stats.functions.keys())
logger = tools.EvolutionLogger(column_names)
logger.logHeader()
ngen = 200
g = 0
schematas = nicheSchematas(TARGET_TYPE, IND_SIZE)
for i in range(TARGET_TYPE):
size = int(TARGET_SIZE/TARGET_TYPE)
target_set.extend(toolbox.target_set(schematas[i], size))
species.append(toolbox.species())
# Init with a random representative for each species
representatives = [random.choice(s) for s in species]
while g < ngen:
# Initialize a container for the next generation representatives
next_repr = [None] * len(species)
for i, s in enumerate(species):
# Variate the species individuals
s = algorithms.varAnd(s, toolbox, 0.6, 1.0)
# Get the representatives excluding the current species
r = representatives[:i] + representatives[i+1:]
for ind in s:
ind.fitness.values = toolbox.evaluate([ind] + r, target_set)
stats.update(s, index=i)
if verbose:
logger.logGeneration(gen=g, species=i, evals=len(s), stats=stats, index=i)
# Select the individuals
species[i] = toolbox.select(s, len(s)) # Tournament selection
next_repr[i] = toolbox.get_best(s)[0] # Best selection
g += 1
representatives = next_repr
if extended:
for r in representatives:
print("".join(str(x) for x in r))
def runCoEA(toolbox, stats, logbook, numGen=100, rnd=False, cxp=0.6, mutp=1.0, **kwargs):
"""Initializes and runs the coevolutionary algorithm.
:returns: the best individual of the run."""
# RUN IT
log.info("CxP: %f; MutP: %f" % (cxp, mutp))
log.info("Creating the population...")
NUMSPECIES = 2
species_index = list(range(NUMSPECIES))
species = [toolbox.species() for _ in range(NUMSPECIES)]
representatives = [random.choice(species[i]) for i in range(NUMSPECIES)]
representatives[0].fitness.values = (toolbox.evaluate(representatives, curspecies=0),)
representatives[1].fitness.values = (toolbox.evaluate(representatives[::-1], curspecies=1),)
# pop = toolbox.population(n=4)
bestsofar = [random.choice(species[i]) for i in range(NUMSPECIES)]
bestsofar[0].fitness.values = (toolbox.evaluate(bestsofar, curspecies=0),)
bestsofar[1].fitness.values = (toolbox.evaluate(bestsofar[::-1], curspecies=1),)
log.info("Running the algorithm...")
for g in xrange(numGen):
# Initialize a container for the next generation representatives
next_repr = [None] * len(species)
for (i, s), j in zip(enumerate(species), species_index):
# Vary the species individuals
s = algorithms.varAnd(s, toolbox, cxp, mutp)
# Get the representatives excluding the current species
r = representatives[:i] + representatives[i + 1 :]
for ind in s:
log.debug("Evaluating species %d" % (j,))
log.debug(r)
# Evaluate and set the individual fitness
ind.fitness.values = (toolbox.evaluate([ind] + r, curspecies=j),)
# Select the individuals
species[i] = toolbox.select(s, len(s)) # Tournament selection
if not rnd:
next_repr[i] = toolbox.get_best(species[i])[0] # Best selection
else:
next_repr[i] = random.choice(species[i])
# Update stats
record = stats.compile(s)
logbook.record(gen=g, species=j, evals=len(s), **record)
log.info(logbook.stream)
for i in species_index:
if next_repr[i].fitness.values <= representatives[i].fitness.values:
representatives[i] = next_repr[i]
# for index in range(len(representatives)):
if representatives[i].fitness.values < bestsofar[i].fitness.values:
bestsofar[i] = representatives[i]
log.info("Done!\n")
log.info(bestsofar[0])
log.info(bestsofar[1])
return bestsofar
def main():
random.seed(64)
NBR_DEMES = 3
MU = 300
NGEN = 40
CXPB = 0.5
MUTPB = 0.2
MIG_RATE = 5
demes = [toolbox.population(n=MU) for _ in range(NBR_DEMES)]
hof = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: ind.fitness.values, 4)
stats.register("avg", tools.mean)
stats.register("std", tools.std)
stats.register("min", min)
stats.register("max", max)
column_names = ["gen", "deme", "evals"]
column_names.extend(stats.functions.keys())
logger = tools.EvolutionLogger(column_names)
logger.logHeader()
for idx, deme in enumerate(demes):
for ind in deme:
ind.fitness.values = toolbox.evaluate(ind)
stats.update(deme, idx)
hof.update(deme)
logger.logGeneration(gen="0", deme=idx, evals=len(deme), stats=stats, index=idx)
stats.update(demes[0]+demes[1]+demes[2], 3)
logger.logGeneration(gen=0, deme=idx, evals="-", stats=stats, index=3)
gen = 1
while gen <= NGEN and stats.max[3][-1][0] < 100.0:
for idx, deme in enumerate(demes):
deme[:] = toolbox.select(deme, len(deme))
deme[:] = algorithms.varAnd(deme, toolbox, cxpb=CXPB, mutpb=MUTPB)
invalid_ind = [ind for ind in deme if not ind.fitness.valid]
for ind in invalid_ind:
ind.fitness.values = toolbox.evaluate(ind)
stats.update(deme, idx)
hof.update(deme)
logger.logGeneration(gen="%d" %gen, deme=idx, evals=len(invalid_ind), stats=stats, index=idx)
if gen % MIG_RATE == 0:
toolbox.migrate(demes)
stats.update(demes[0]+demes[1]+demes[2], 3)
logger.logGeneration(gen="%d" % gen, deme="-", evals="-", stats=stats, index=3)
gen += 1
return demes, stats, hof
def gen_new_offspring():
valid_offspring = True
offspring = None
while valid_offspring:
# select two individuals and clone them
offspring = map(toolbox.clone, toolbox.select(population, 2))
# apply crossover and mutation, take the first offspring
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)[0]
valid_offspring = offspring.fitness.valid
# if the offspring is valid it is already in the population
return offspring
def _evolve(self, measure, population, toolbox, ngen, cxpb, mutpb,
verbose=True):
''' Main evolution algorithm. A tweaked version of the eaSimple
algorithm included in the DEAP package that adds per-generation logging
of the best individual's properties and drops all the
Statistics/HallOfFame stuff (since we're handling that ourselves). See
DEAP documentation of algorithms.eaSimple() for all arguments.
'''
# if verbose:
# column_names = ["gen", "evals"]
# if stats is not None:
# column_names += stats.functions.keys()
# logger = tools.Logbook(column_names)
# logger.logHeader()
# logger.logGeneration(evals=len(population), gen=0, stats=stats)
# Begin the generational process
for gen in range(0, ngen):
# Select the next generation individuals
offspring = toolbox.select(population, k=len(population))
# Variate the pool of individuals
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Replace the current population by the offspring
offspring = sorted(
offspring, key=lambda x: x.fitness, reverse=True)
population[:] = offspring
# Save best individual as an AbbreviatedMeasure
self.best_individuals.append(population[0])
best_abb = AbbreviatedMeasure(
self.measure, population[0], abbreviator=self.abbreviator,
evaluator=self.evaluator, stats=True)
self.best_measures.append(best_abb)
r_squared = np.round(best_abb.r_squared.mean(), 2)
n_items = np.sum(population[0])
# Update the statistics with the new population
if self.stats is not None:
record = self.stats.compile(population)
self.logbook.record(
gen=gen, r_squared=r_squared, n_items=n_items, **record)
# Save last population in case we want to resume
self.pop = population
def main():
if os.path.isfile(CP):
# A file name has been given, then load the data from the file
cp = read_checkpoint()
population = cp["population"]
start_gen = cp["generation"] + 1
halloffame = cp["halloffame"]
logbook = cp["logbook"]
random.setstate(cp["rndstate"])
else:
# Start a new evolution
random.seed()
population = toolbox.population(n=300)
start_gen = 0
halloffame = tools.HallOfFame(maxsize=1)
logbook = tools.Logbook()
stats_fit = tools.Statistics(lambda ind: ind.fitness.values)
stats_size = tools.Statistics(len)
mstats = tools.MultiStatistics(fitness=stats_fit, size=stats_size)
mstats.register("avg", numpy.mean)
mstats.register("std", numpy.std)
mstats.register("min", numpy.min)
mstats.register("max", numpy.max)
#algorithms.eaSimple(pop, toolbox, 0.5, 0.2, NGEN, mstats, halloffame=hof)
#print(hof[0])
begin = start_gen
end = begin + NGEN
print("begin: {}, end: {}".format(begin, end))
for gen in range(begin, end):
population = algorithms.varAnd(population, toolbox, cxpb=toolbox.mate, mutpb=toolbox.mutate)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
halloffame.update(population)
record = mstats.compile(population)
logbook.record(gen=gen, evals=len(invalid_ind), **record)
population = toolbox.select(population, k=len(population))
if (gen + 1) % FREQ == 0 or gen == end - 1:
# Fill the dictionary using the dict(key=value[, ...]) constructor
cp = dict(population=population, generation=gen, halloffame=halloffame,
logbook=logbook, rndstate=random.getstate())
with open(CP, "wb") as cp_file:
pickle.dump(cp, cp_file, -1)
def evolve_machines(POP):
population = POP
offspring = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, population)
for fit, ind in zip(fits, population):
ind.fitness = fit
population = toolbox.select(population, k=len(population))
top10 = tools.selBest(population, k=10)
return population
def main(extended=True, verbose=True):
target_set = []
species = []
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", numpy.mean)
stats.register("std", numpy.std)
stats.register("min", numpy.min)
stats.register("max", numpy.max)
logbook = tools.Logbook()
logbook.header = "gen", "species", "evals", "std", "min", "avg", "max"
ngen = 200
g = 0
schematas = nicheSchematas(TARGET_TYPE, IND_SIZE)
for i in range(TARGET_TYPE):
size = int(TARGET_SIZE/TARGET_TYPE)
target_set.extend(toolbox.target_set(schematas[i], size))
species.append(toolbox.species())
# Init with a random representative for each species
representatives = [random.choice(s) for s in species]
while g < ngen:
# Initialize a container for the next generation representatives
next_repr = [None] * len(species)
for i, s in enumerate(species):
# Vary the species individuals
s = algorithms.varAnd(s, toolbox, 0.6, 1.0)
# Get the representatives excluding the current species
r = representatives[:i] + representatives[i+1:]
for ind in s:
ind.fitness.values = toolbox.evaluate([ind] + r, target_set)
record = stats.compile(s)
logbook.record(gen=g, species=i, evals=len(s), **record)
if verbose:
print(logbook.stream)
# Select the individuals
species[i] = toolbox.select(s, len(s)) # Tournament selection
next_repr[i] = toolbox.get_best(s)[0] # Best selection
g += 1
representatives = next_repr
if extended:
for r in representatives:
print("".join(str(x) for x in r))
def main(procid, pipein, pipeout, sync, seed=None):
random.seed(seed)
toolbox.register("migrate", migPipe, k=5, pipein=pipein, pipeout=pipeout,
selection=tools.selBest, replacement=random.sample)
MU = 300
NGEN = 40
CXPB = 0.5
MUTPB = 0.2
MIG_RATE = 5
deme = toolbox.population(n=MU)
hof = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", numpy.mean)
stats.register("std", numpy.std)
stats.register("min", numpy.min)
stats.register("max", numpy.max)
logbook = tools.Logbook()
logbook.header = "gen", "deme", "evals", "std", "min", "avg", "max"
for ind in deme:
ind.fitness.values = toolbox.evaluate(ind)
record = stats.compile(deme)
logbook.record(gen=0, deme=procid, evals=len(deme), **record)
hof.update(deme)
if procid == 0:
# Synchronization needed to log header on top and only once
print(logbook.stream)
sync.set()
else:
logbook.log_header = False # Never output the header
sync.wait()
print(logbook.stream)
for gen in range(1, NGEN):
deme = toolbox.select(deme, len(deme))
deme = algorithms.varAnd(deme, toolbox, cxpb=CXPB, mutpb=MUTPB)
invalid_ind = [ind for ind in deme if not ind.fitness.valid]
for ind in invalid_ind:
ind.fitness.values = toolbox.evaluate(ind)
hof.update(deme)
record = stats.compile(deme)
logbook.record(gen=gen, deme=procid, evals=len(deme), **record)
print(logbook.stream)
if gen % MIG_RATE == 0 and gen > 0:
toolbox.migrate(deme)
def train(self, pop = 20, gen = 10):
from deap import algorithms
from deap import base
from deap import creator
from deap import tools
from deap.tools import Statistics
# import random
from scipy.stats import rv_discrete
# creator.create("FitnessMulti", base.Fitness, weights=(1.0, -1.0))
# creator.create("Individual", list, fitness=creator.FitnessMulti)
creator.create("FitnessMin", base.Fitness, weights=(-1.0,))
creator.create("Individual", list, fitness=creator.FitnessMin)
toolbox = base.Toolbox()
# Attribute generator
custm = rv_discrete(name='custm', values=(self.a_w.index, self.a_w.values))
toolbox.register("attr_int", custm.rvs)
# Structure initializers
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_int, n=len(self.s))
toolbox.register("population", tools.initRepeat, list, toolbox.individual, n=pop)
# Operator registering
toolbox.register("evaluate", self.eval_classifer)
toolbox.register("mate", tools.cxUniform, indpb=0.5)
toolbox.register("mutate", tools.mutUniformInt, low=min(self.a.index), up=max(self.a.index), indpb=0.1)
toolbox.register("select", tools.selNSGA2)
MU, LAMBDA = pop, pop
population = toolbox.population(n=MU)
hof = tools.ParetoFront()
s = Statistics(key=lambda ind: ind.fitness.values)
s.register("mean", np.mean)
s.register("min", min)
# pop, logbook = algorithms.eaMuPlusLambda(pop, toolbox, mu=MU, lambda_=LAMBDA, cxpb=0.7, mutpb=0.3, ngen=gen, stats=s, halloffame=hof)
for i in range(gen):
offspring = algorithms.varAnd(population, toolbox, cxpb=0.95, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = tools.selBest(offspring, int(0.05*len(offspring))) + tools.selTournament(offspring, len(offspring)-int(0.05*len(offspring)), tournsize=3)
# population = toolbox.select(offspring, k=len(population))
print s.compile(population)
top10 = tools.selBest(population, k=10)
return top10
def main(procid, pipein, pipeout, sync, seed=None):
random.seed(seed)
toolbox.register(
"migrate", migPipe, k=5, pipein=pipein, pipeout=pipeout, selection=tools.selBest, replacement=random.sample
)
MU = 300
NGEN = 100
CXPB = 0.8
MUTPB = 1
MIG_RATE = 5
deme = toolbox.population(n=MU)
hof = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", tools.mean)
stats.register("std", tools.std)
stats.register("min", min)
stats.register("max", max)
logger = tools.EvolutionLogger(["gen", "deme", "evals"] + stats.functions.keys())
if procid == 0:
# Synchronization needed to log header on top and only once
logger.logHeader()
sync.set()
else:
sync.wait()
for ind in deme:
ind.fitness.values = toolbox.evaluate(ind)
stats.update(deme)
hof.update(deme)
logger.logGeneration(gen="0", deme=procid, evals=len(deme), stats=stats)
for gen in range(1, NGEN):
deme = toolbox.select(deme, len(deme))
deme = algorithms.varAnd(deme, toolbox, cxpb=CXPB, mutpb=MUTPB)
invalid_ind = [ind for ind in deme if not ind.fitness.valid]
for ind in invalid_ind:
ind.fitness.values = toolbox.evaluate(ind)
stats.update(deme)
hof.update(deme)
logger.logGeneration(gen="%d" % gen, deme=procid, evals=len(invalid_ind), stats=stats)
if gen % MIG_RATE == 0 and gen > 0:
toolbox.migrate(deme)
print "Best individual: " + str(convertArrToFloat(hof[-1]))
print "Rastrigin value: " + str(rastrigin_arg0(hof[-1])[0]) + "\n\n\n"
def train(self, pop = 20, gen = 10):
from deap import algorithms
from deap import base
from deap import creator
from deap import tools
import random
import numpy as np
from deap.tools import Statistics
# creator.create("FitnessMulti", base.Fitness, weights=(1.0, -1.0))
# creator.create("Individual", list, fitness=creator.FitnessMulti)
creator.create("FitnessMax", base.Fitness, weights=(1.0,))
creator.create("Individual", list, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
# Attribute generator
toolbox.register("attr_bool", random.randint, 0, 1)
# Structure initializers
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_bool, n=len(self.X.columns))
toolbox.register("population", tools.initRepeat, list, toolbox.individual, n=pop)
# Operator registering
toolbox.register("evaluate", self.eval_classifer)
toolbox.register("mate", tools.cxUniform, indpb=0.1)
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
# toolbox.register("select", tools.selNSGA2)
MU, LAMBDA = pop, pop
population = toolbox.population(n=MU)
# hof = tools.ParetoFront()
s = Statistics(key=lambda ind: ind.fitness.values)
s.register("mean", np.mean)
s.register("max", max)
# pop, logbook = algorithms.eaMuPlusLambda(pop, toolbox, mu=MU, lambda_=LAMBDA, cxpb=0.7, mutpb=0.3, ngen=gen, stats=s, halloffame=hof)
for i in range(gen):
offspring = algorithms.varAnd(population, toolbox, cxpb=0.95, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = tools.selBest(offspring, int(0.05*len(offspring))) + tools.selTournament(offspring, len(offspring)-int(0.05*len(offspring)), tournsize=3)
# population = toolbox.select(offspring, k=len(population))
print s.compile(population)
top10 = tools.selBest(population, k=10)
print top10
return top10[0]
def eaSimple(population, toolbox, cxpb, mutpb, ngen, stats=None,
halloffame=None, verbose=__debug__):
logbook = tools.Logbook()
logbook.header = ['gen', 'nevals'] + (stats.fields if stats else [])
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
if halloffame is not None:
halloffame.update(population)
record = stats.compile(population) if stats else {}
logbook.record(gen=0, nevals=len(invalid_ind), **record)
if verbose:
print logbook.stream
# Begin the generational process
gen = 1
while evalNumThreaten(tools.selBest(population, k=1)[0])[0] != 0:
gen += 1
# Select the next generation individuals
offspring = toolbox.select(population, len(population))
# Vary the pool of individuals
offspring = algorithms.varAnd(offspring, toolbox, cxpb, mutpb)
# Evaluate the individuals with an invalid fitness
invalid_ind = [ind for ind in offspring if not ind.fitness.valid]
fitnesses = toolbox.map(toolbox.evaluate, invalid_ind)
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = fit
# Update the hall of fame with the generated individuals
if halloffame is not None:
halloffame.update(offspring)
# Replace the current population by the offspring
population[:] = offspring
# Append the current generation statistics to the logbook
record = stats.compile(population) if stats else {}
logbook.record(gen=gen, nevals=len(invalid_ind), **record)
if verbose:
print logbook.stream
print 'total generations is',gen
return population, logbook
def main():
random.seed(64)
NBR_DEMES = 3
MU = 300
NGEN = 40
CXPB = 0.5
MUTPB = 0.2
MIG_RATE = 5
demes = [toolbox.population(n=MU) for _ in range(NBR_DEMES)]
hof = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", numpy.mean)
stats.register("std", numpy.std)
stats.register("min", numpy.min)
stats.register("max", numpy.max)
logbook = tools.Logbook()
logbook.header = "gen", "deme", "evals", "std", "min", "avg", "max"
for idx, deme in enumerate(demes):
for ind in deme:
ind.fitness.values = toolbox.evaluate(ind)
logbook.record(gen=0, deme=idx, evals=len(deme), **stats.compile(deme))
hof.update(deme)
print(logbook.stream)
gen = 1
while gen <= NGEN and logbook[-1]["max"] < 100.0:
for idx, deme in enumerate(demes):
deme[:] = toolbox.select(deme, len(deme))
deme[:] = algorithms.varAnd(deme, toolbox, cxpb=CXPB, mutpb=MUTPB)
invalid_ind = [ind for ind in deme if not ind.fitness.valid]
for ind in invalid_ind:
ind.fitness.values = toolbox.evaluate(ind)
logbook.record(gen=gen, deme=idx, evals=len(
deme), **stats.compile(deme))
hof.update(deme)
print(logbook.stream)
if gen % MIG_RATE == 0:
toolbox.migrate(demes)
gen += 1
return demes, logbook, hof
def main(seed=None):
random.seed(seed)
node = Node()
toolbox.register("migrate", migRingMPI, k=5, node=node,
selection=tools.selBest, replacement=random.sample)
MU = 300
NGEN = 200
CXPB = 0.5
MUTPB = 0.2
MIG_RATE = 5
deme = toolbox.population(n=MU)
hof = tools.HallOfFame(1)
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("avg", tools.mean)
stats.register("std", tools.std)
stats.register("min", min)
stats.register("max", max)
logger = tools.EvolutionLogger(["gen", "deme", "evals"] + stats.functions.keys())
if rank == 0:
# Synchronization needed to log header on top and only once
logger.logHeader()
comm.Barrier()
for ind in deme:
ind.fitness.values = toolbox.evaluate(ind)
stats.update(deme)
hof.update(deme)
logger.logGeneration(gen="0", deme=rank, evals=len(deme), stats=stats)
for gen in range(1, NGEN):
deme = toolbox.select(deme, len(deme))
deme = algorithms.varAnd(deme, toolbox, cxpb=CXPB, mutpb=MUTPB)
invalid_ind = [ind for ind in deme if not ind.fitness.valid]
for ind in invalid_ind:
ind.fitness.values = toolbox.evaluate(ind)
stats.update(deme)
hof.update(deme)
logger.logGeneration(gen="%d" % gen, deme=rank, evals=len(invalid_ind), stats=stats)
if gen % MIG_RATE == 0 and gen > 0:
toolbox.migrate(deme)
def run(self):
meta_spec = self.experiment.spec['meta']
ray.init(**meta_spec.get('resources', {}))
max_generation = meta_spec['max_generation']
pop_size = meta_spec['max_trial'] or calc_population_size(self.experiment)
logger.info(f'EvolutionarySearch max_generation: {max_generation}, population size: {pop_size}')
trial_data_dict = {}
config_hash = {} # config hash_str to trial_index
toolbox = self.init_deap()
population = toolbox.population(n=pop_size)
for gen in range(1, max_generation + 1):
logger.info(f'Running generation: {gen}/{max_generation}')
ray_id_to_config = {}
pending_ids = []
for individual in population:
config = dict(individual.items())
hash_str = util.to_json(config, indent=0)
if hash_str not in config_hash:
trial_index = self.experiment.info_space.tick('trial')['trial']
config_hash[hash_str] = config['trial_index'] = trial_index
ray_id = run_trial.remote(self.experiment, config)
ray_id_to_config[ray_id] = config
pending_ids.append(ray_id)
individual['trial_index'] = config_hash[hash_str]
trial_data_dict.update(get_ray_results(pending_ids, ray_id_to_config))
for individual in population:
trial_index = individual.pop('trial_index')
trial_data = trial_data_dict.get(trial_index, {'fitness': 0}) # if trial errored
individual.fitness.values = trial_data['fitness'],
preview = 'Fittest of population preview:'
for individual in tools.selBest(population, k=min(10, pop_size)):
preview += f'\nfitness: {individual.fitness.values[0]}, {individual}'
logger.info(preview)
# prepare offspring for next generation
if gen < max_generation:
population = toolbox.select(population, len(population))
# Vary the pool of individuals
population = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.5)
ray.worker.cleanup()
return trial_data_dict
def genetic_keyboard(pop_num, gen_num, input_pop=None):
#What creator.create does is that it creates a new class. Its name is the first argument of the function.
# Here on the first line we create a class named FitnessMax().base.Fitness tells you that this class is derived from the class base.Fitness().weight() is explained in the tutorial.
creator.create("FitnessMin", base.Fitness, weights=(-1.0,))
# On the second line we create a class named Individual() derived from a list. We add the class creator.Fitness as one of its additionnal attribute.
creator.create("Individual", list, fitness=creator.FitnessMin)
toolbox = base.Toolbox()
toolbox.register("indices", random.sample, range(len(CHARACTERS)), len(CHARACTERS))
# container – The type to put in the data from func.
# generator – A function returning an iterable (list, tuple, ...), the content of this iterable will fill the container.
toolbox.register("individual", tools.initIterate, creator.Individual,
toolbox.indices)
toolbox.register("population", tools.initRepeat, list,
toolbox.individual)
toolbox.register("evaluate", frequencyFitness)
#ordered crossover
toolbox.register("mate", tools.cxOrdered)
#mutation we will swap elements from two points of the individual.
toolbox.register("mutate", tools.mutShuffleIndexes, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)
# result, log = algorithms.eaSimple(population, toolbox,
# cxpb=0.8, mutpb=0.2,
# gen_num=400, verbose=False)
# best_individual = tools.selBest(result, k=1)[0]
# pop_num = 100
# gen_num=100
population = toolbox.population(n=pop_num)
with open('deap_results', 'w') as f:
for gen in range(gen_num):
offspring = algorithms.varAnd(population, toolbox,
cxpb=0.5, mutpb=0.1)
fits = toolbox.map(toolbox.evaluate, offspring)
for fit, ind in zip(fits, offspring):
ind.fitness.values = fit
population = toolbox.select(offspring, k=len(population))
# best_individual = tools.selBest(population, k=1)[0]
# f.write(str(gen) + ' ' + str(frequencyFitness(best_individual)) +
# ' ' + str(indices_to_keyboard(best_individual)))
# f.write('\n')
return population
